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- PDB-1l8a: E. COLI PYRUVATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1l8a
TitleE. COLI PYRUVATE DEHYDROGENASE
ComponentsPyruvate dehydrogenase E1 component
KeywordsOXIDOREDUCTASE / THIAMIN DIPHOSPHATE / PYRUVATE / ALPHA-KETO ACID DEHYDROGENASE
Function / homology
Function and homology information


: / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity / magnesium ion binding ...: / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / metal ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / : / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Rossmann fold - #920 ...Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / : / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Rossmann fold - #920 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Pyruvate dehydrogenase E1 component / Pyruvate dehydrogenase E1 component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsFurey, W. / Arjunan, P.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution.
Authors: Arjunan, P. / Nemeria, N. / Brunskill, A. / Chandrasekhar, K. / Sax, M. / Yan, Y. / Jordan, F. / Guest, J.R. / Furey, W.
History
DepositionMar 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,2146
Polymers199,3142
Non-polymers8994
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-58 kcal/mol
Surface area48880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.690, 141.600, 82.460
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains a functional dimer, with the two identical molecules related by a non-crystallographic twofold axis. It also contains two thiamin diphosphate and two magnesium II ion cofactors.

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Components

#1: Protein Pyruvate dehydrogenase E1 component


Mass: 99657.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: JRG pGS878 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 3456
References: UniProt: P06958, UniProt: P0AFG8*PLUS, pyruvate dehydrogenase (acetyl-transferring)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.05
Details: PEG2000 monomethyl ether, propanol, sodium azide, Hepes buffer, magnesium chloride, thiamin diphosphate, pH 7.05, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115-20 %PEG2000 MME1reservoir
210 %propanol1reservoir
30.2 %1reservoirNaN3
460 mMHEPES1reservoirpH7.05

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.072 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jan 27, 2000 / Details: toroidal mirror
RadiationMonochromator: curved silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 146183 / Num. obs: 146183 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 17.9
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.9 / Num. unique all: 13132 / Rsym value: 0.175 / % possible all: 70.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 528145 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 70.2 % / Rmerge(I) obs: 0.175

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 8098 6 %RANDOM
Rwork0.189 ---
all0.198 144190 --
obs0.192 133768 85.4 %-
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12682 0 54 682 13418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.273
X-RAY DIFFRACTIONx_dihedral_angle_d24.92
X-RAY DIFFRACTIONx_improper_angle_d0.709
X-RAY DIFFRACTIONx_mcbond_it1.411.5
X-RAY DIFFRACTIONx_mcangle_it2.12
X-RAY DIFFRACTIONx_scbond_it2.712
X-RAY DIFFRACTIONx_scangle_it4.062.5
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2607 674 6 %
Rwork0.2361 10993 -
obs-11667 62.2 %
Refinement
*PLUS
Num. reflection obs: 125670 / Rfactor all: 0.198 / Rfactor obs: 0.192 / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.709
LS refinement shell
*PLUS
Rfactor Rfree: 0.261 / % reflection Rfree: 6 % / Rfactor Rwork: 0.236

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